Author details

Full Name

Sagar D Khare

Affiliation

The State University of New Jersey

ORCID

Career Start Year

2003

Papers

H Index

Expertise

CM4AI Collaborator

Andrej Sali (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36824945	Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network.	bioRxiv	2023
37521667	Genetic Encoding of Arylazopyrazole Phenylalanine for Optical Control of Translation.	ACS Omega	2023
37701412	Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032].	Heliyon	2023
37729196	Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network.	Proc Natl Acad Sci U S A	2023
37060757	Multifaceted interactions mediated by intrinsically disordered regions play key roles in alpha synuclein aggregation.	Curr Opin Struct Biol	2023
37035348	Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus.	Heliyon	2023
37030124	A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly.	J Inorg Biochem	2023
36996092	Monomer Choice Influences <i>N</i>-Acryloyl Amino Acid Grafter Conversion via Protease Catalysis.	Biomacromolecules	2023
36778399	A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic.	bioRxiv	2023
34580920	Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.	Proteins	2022
35511693	Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection.	Mol Biol Evol	2022
35612958	Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization.	Biochemistry	2022
35377786	Massively parallel, computationally guided design of a proenzyme.	Proc Natl Acad Sci U S A	2022
35776893	Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign.	ACS Chem Biol	2022
36474933	Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.	Biophys Rev	2022
35974764	Highly stereoselective and enantiodivergent synthesis of cyclopropylphosphonates with engineered carbene transferases.	Chem Sci	2022
35107997	Enantioselective Synthesis of Î±-Trifluoromethyl Amines via Biocatalytic N-H Bond Insertion with Acceptor-Acceptor Carbene Donors.	J Am Chem Soc	2022
33969560	Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans.	Protein Sci	2021
33900750	MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform.	J Chem Inf Model	2021
33661634	Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties.	J Phys Chem B	2021
34931193	Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces.	bioRxiv	2021
32483333	Macromolecular modeling and design in Rosetta: recent methods and frameworks.	Nat Methods	2020
32017536	Mathematical Models of Protease-Based Enzymatic Biosensors.	ACS Synth Biol	2020
32175488	Protease-Catalyzed l-Aspartate Oligomerization: Substrate Selectivity and Computational Modeling.	ACS Omega	2020
32569994	Recent progress in designing protein-based supramolecular assemblies.	Curr Opin Struct Biol	2020
30587591	Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.	Proc Natl Acad Sci U S A	2019
32856001	Photoswitchable affinity reagents: Computational design and efficient red-light switching.	ChemPhotoChem	2019
31209296	Stimulus-responsive self-assembly of protein-based fractals by computational design.	Nat Chem	2019
29250820	A computational method for the design of nested proteins by loop-directed domain insertion.	Proteins	2018
30240210	Systematic Comparison of Amber and Rosetta Energy Functions for Protein Structure Evaluation.	J Chem Theory Comput	2018
29782835	Multi-Pronged Interactions Underlie Inhibition of Î±-Synuclein Aggregation by Î²-Synuclein.	J Mol Biol	2018
29414047	Computational assessment of thioether isosteres.	J Mol Graph Model	2018
29251923	Computational Design of a Photocontrolled Cytosine Deaminase.	J Am Chem Soc	2018
27914062	Computational Design of Ligand Binding Proteins.	Methods Mol Biol	2017
28160000	Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme.	Protein Eng Des Sel	2017
29109284	Enzyme stabilization via computationally guided protein stapling.	Proc Natl Acad Sci U S A	2017
28650961	MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory.	PLoS Comput Biol	2017
28513090	Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces.	Protein Sci	2017
28799209	Computation-Guided Design of a Stimulus-Responsive Multienzyme Supramolecular Assembly.	Chembiochem	2017
28893989	Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.	Proc Natl Acad Sci U S A	2017
28759213	Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Interaction.	J Am Chem Soc	2017
28710275	A pH-dependent switch promotes Î²-synuclein fibril formation via glutamate residues.	J Biol Chem	2017
27932294	Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design.	J Mol Biol	2017
27094290	Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments.	Methods Mol Biol	2016
26449207	Structural principles for computational and de novo design of 4Fe-4S metalloproteins.	Biochim Biophys Acta	2016
26419257	CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.	J Chem Inf Model	2016
27094291	Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids.	Methods Mol Biol	2016
26714017	Introduction to the Rosetta Special Collection.	PLoS One	2015
26529612	FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.	PLoS Comput Biol	2015
25213421	Computational redesign of metalloenzymes for catalyzing new reactions.	Methods Mol Biol	2014

1 - 50 of 71

James S Fraser

University of California san francisco

Career Start Year 2006

Number of shared co-authors 12

Henry van den Bedem

University of California San Francisco

Career Start Year 2002

Number of shared co-authors 2

Matteo Dal Peraro

Institute of Bioengineering

Career Start Year 2001

Number of shared co-authors 10

Hao Fan

College of Biotechnology and Bioengineering, Zhejiang University of Technology

Career Start Year 2001

Number of shared co-authors 3

Lewyn Li

Dana-Farber Cancer Institute, Harvard Medical School

Career Start Year 2000

Number of shared co-authors 1

Matthew P Jacobson

Department of Pharmaceutical Chemistry, University of California san francisco

Career Start Year 1999

Number of shared co-authors 12

Efrat Ben-Zeev

Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science

Career Start Year 1999

Number of shared co-authors 5

David R Hall

Diamond Light Source Ltd, Harwell Science & Innovation Campus

Career Start Year 1998

Number of shared co-authors 7

Soumya S Ray

Lysosomal Therapeutics Inc.

Career Start Year 1997

Number of shared co-authors 2

Jeffery G Saven

University of Pennsylvania

Career Start Year 1996

Number of shared co-authors 1

Michele Vendruscolo

University of Cambridge

Career Start Year 1996

Number of shared co-authors 7

Mallur S Madhusudhan

Indian Institute of Science Education and Research Pune

Career Start Year 1996

Number of shared co-authors 2

Shira Albeck

Weizmann Institute of Science

Career Start Year 1996

Number of shared co-authors 9

Orly Dym

Weizmann Institute of Science

Career Start Year 1995

Number of shared co-authors 8

Ivet Bahar

Laufer Center for Physical and Quantitative Biology, Stony Brook University

Career Start Year 1994

Number of shared co-authors 3

Giorgio Colombo

Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

Career Start Year 1993

Number of shared co-authors 0

Carlos J Camacho

University of Pittsburgh

Career Start Year 1990

Number of shared co-authors 4

Ram Samudrala

Jacobs School of Medicine and Biomedical Sciences, University at Buffalo

Career Start Year 1990

Number of shared co-authors 2

Rebecca C Wade

Center for Molecular Biology (ZMBH), Heidelberg University

Career Start Year 1989

Number of shared co-authors 6

Steven C Almo

Albert Einstein College of Medicine

Career Start Year 1988

Number of shared co-authors 11

Miriam Eisenstein

Weizmann Institute of Science

Career Start Year 1988

Number of shared co-authors 5

Piotr Cieplak

Sanford-Burnham-Prebys Medical Discovery Institute

Career Start Year 1987

Number of shared co-authors 1

William F DeGrado

Department of Pharmaceutical Chemistry, University of California san francisco

Career Start Year 1982

Number of shared co-authors 5

Sandor Vajda

Boston University

Career Start Year 1982

Number of shared co-authors 14

Ruth Nussinov

Sackler School of Medicine, Tel Aviv University

Career Start Year 1980

Number of shared co-authors 14

Charles L Brooks

University of Michigan ann arbor

Career Start Year 1974

Number of shared co-authors 2

Tom L Blundell

Heartand Lung Research Institute, University of Cambridge

Career Start Year 1971

Number of shared co-authors 3

Michael Levitt

Stanford University

Career Start Year 1969

Number of shared co-authors 12

Andras Fiser

Albert Einstein College of Medicine

Career Start Year 1968

Number of shared co-authors 15

David Eisenberg

university of california los angeles

Career Start Year 1963

Number of shared co-authors 1

row(s) 1 - 30 of 30

David Baker

University of Washington

Co-authored papers 13

Nikolay V Dokholyan

Pennsylvania State University College of Medicine

Co-authored papers 10

Stephen K Burley

The State University of New Jersey

Co-authored papers 5

Brian P Hudson

The State University of New Jersey

Co-authored papers 3

Christine Zardecki

The State University of New Jersey

Co-authored papers 3

Jeffrey J Gray

Johns Hopkins University

Co-authored papers 3

Sarel J Fleishman

Co-authored papers 3

Roland L Dunbrack

Fox Chase Cancer Center

Co-authored papers 3

Wadih Arap

Rutgers Cancer Institute of New Jersey

Co-authored papers 2

Liang Tong

Columbia University

Co-authored papers 2

Vijaya L Simhadri

Center for Biologics Evaluation and Research

Co-authored papers 2

Eric J Moore

2Mayo Clinic

Co-authored papers 2

Jens Meiler

Vanderbilt University

Co-authored papers 2

John D Westbrook

The State University of New Jersey

Co-authored papers 2

Renata Pasqualini

Rutgers Cancer Institute of New Jersey

Co-authored papers 2

Rhiju Das

Stanford University School of Medicine

Co-authored papers 2

Eduardo D Sontag

Co-authored papers 2

David A Case

Rutgers University

Co-authored papers 1

Jaroslav Bendl

Co-authored papers 1

Joel L Sussman

Weizmann Institute of Science

Co-authored papers 1

Gaetano T Montelione

Rensselaer Polytechnic Institute

Co-authored papers 1

Noah Ollikainen

California Institute of Technology

Co-authored papers 1

Grigore Pintilie

Stanford University

Co-authored papers 1

Nir London

The Weizmann Institute of Science

Co-authored papers 1

Sophia K Tan

University of California san francisco

Co-authored papers 1

Brian G Pierce

University of Maryland Institute for Bioscience and Biotechnology Research

Co-authored papers 1

David S Goodsell

The State University of New Jersey

Co-authored papers 1

Hahnbeom Park

Co-authored papers 1

Richard Bonneau

Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation

Co-authored papers 1

Jeliazko R Jeliazkov

Co-authored papers 1

1 - 30

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